We have some DNA extractions from human cheek cells that are (not surprisingly) contaminated with bacterial DNA. I would like to separate out the bacterial DNA and leave just the human genomic DNA. This could obviously be done by size (gel or column purification). Can anyone out there recommend a kit or protocol that effectively separates human gDNA from all smaller DNA's? Cheap and easy would be great! Any input would be appreciated.

-DrAnnie-

i'm not a specialist on that issue ...and as far as i know this is not an easy task ...since the sequencing of e.g. the Neanderthaler was hampered by the contamination of the DNA with prokaryotic DNA.

But maybe you can resolve your eukaryotic DNA from the prokaryotic DNA using Pulsed field gel electrophoresis ...since your human DNA should be less degraded!